2016
Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition
Gagnon MG, Roy RN, Lomakin IB, Florin T, Mankin AS, Steitz TA. Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. Nucleic Acids Research 2016, 44: 2439-2450. PMID: 26809677, PMCID: PMC4797290, DOI: 10.1093/nar/gkw018.Peer-Reviewed Original ResearchAmino Acid SequenceAnimalsAnti-Bacterial AgentsAntimicrobial Cationic PeptidesBinding SitesCattleCrystallography, X-RayEscherichia coliInsect ProteinsModels, MolecularMolecular Sequence DataPeptides, CyclicProtein BindingProtein BiosynthesisRibosomesRNA, MessengerRNA, TransferSpecies SpecificityThermus thermophilus
2003
Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase
Laptenko O, Lee J, Lomakin I, Borukhov S. Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. The EMBO Journal 2003, 22: 6322-6334. PMID: 14633991, PMCID: PMC291851, DOI: 10.1093/emboj/cdg610.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCatalysisCross-Linking ReagentsDNA-Directed RNA PolymerasesEndoribonucleasesEscherichia coliEscherichia coli ProteinsHydroxyl RadicalModels, MolecularMolecular Sequence DataProtein ConformationProtein SubunitsSequence AlignmentSequence Homology, Amino AcidTranscription FactorsTranscription, GeneticTranscriptional Elongation FactorsConceptsN-terminal coiled-coil domainRNA polymeraseTranscription elongation factors GreANucleolytic activityRNAP secondary channelFirst transcription factorRNA hydrolysisRNAP catalytic centerCoiled-coil domainMolecular genetic methodsTerminal globular domainTranscription elongationTranscriptional pausingTranscription initiationTranscription factorsGenetic methodsKey residuesBiological roleGlobular domainCatalytic componentCatalytic centerGreAPolymeraseCatalytic actSecondary channelEukaryotic Initiation Factors 4G and 4A Mediate Conformational Changes Downstream of the Initiation Codon of the Encephalomyocarditis Virus Internal Ribosomal Entry Site
Kolupaeva VG, Lomakin IB, Pestova TV, Hellen CU. Eukaryotic Initiation Factors 4G and 4A Mediate Conformational Changes Downstream of the Initiation Codon of the Encephalomyocarditis Virus Internal Ribosomal Entry Site. Molecular And Cellular Biology 2003, 23: 687-698. PMID: 12509466, PMCID: PMC151537, DOI: 10.1128/mcb.23.2.687-698.2003.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateBase SequenceBinding SitesCodon, InitiatorEncephalomyocarditis virusEscherichia coliEukaryotic Initiation Factor-4AEukaryotic Initiation Factor-4GGene DeletionModels, BiologicalModels, MolecularMolecular Sequence DataPlasmidsProtein BindingProtein BiosynthesisProtein ConformationProtein Structure, SecondaryProtein Structure, TertiaryRibosomesRNASequence Homology, Nucleic AcidConceptsInternal ribosome entry siteEukaryotic initiation factor 2EIF4GCentral domainEukaryotic initiation factor 4GConformational changesInitiation factor 2K domainRibosome binding siteInitiation of translationInternal ribosomal entry siteEntry siteExtensive conformational rearrangementsThree-way helical junctionInitiation codon AUGRibosome entry siteEncephalomyocarditis virus internal ribosomal entry siteEncephalomyocarditis virus (EMCV) mRNAInitiation codonRibosomal complexesC-terminusIRES functionProductive bindingCodon AUGN-terminus
2000
The Functional Role of Basic Patch, a Structural Element ofEscherichia coli Transcript Cleavage Factors GreA and GreB*
Kulish D, Lee J, Lomakin I, Nowicka B, Das A, Darst S, Normet K, Borukhov S. The Functional Role of Basic Patch, a Structural Element ofEscherichia coli Transcript Cleavage Factors GreA and GreB*. Journal Of Biological Chemistry 2000, 275: 12789-12798. PMID: 10777576, DOI: 10.1074/jbc.275.17.12789.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceDose-Response Relationship, DrugEscherichia coliEscherichia coli ProteinsGenetic Complementation TestHydrogen-Ion ConcentrationIsopropyl ThiogalactosideModels, MolecularMolecular Sequence DataMutagenesisOligonucleotidesPlasmidsRNASequence Homology, Amino AcidTemperatureTranscription FactorsTranscription, GeneticTranscriptional Elongation FactorsConceptsTernary elongation complexTranscript cleavage reactionWild-type factorBasic patchLarge basic patchFunctional roleGre proteinsThermosensitive phenotypeTranscription elongationElongation complexNascent RNAGre factorsThree-dimensional structureRNA polymeraseTerminal domainVivo functionE. coli strainsGreAGreBEscherichia coliType factorsCleavage reactionColi strainsMutantsReadthrough